Antony Holmes, PhD

Associate Research Scientist

Get In Touch

In silico biology.

Antony Holmes is a senior bioinformatics staff scientist and software engineer. He develops and maintains this website, which you can learn more about here.

Selected Publications

1
Super-enhancer hypermutation alters oncogene expression in B cell lymphoma

Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, Dreval K, Wong JCH, Vlasevska S, Corinaldesi C, Soni RK, Basso K, Morin RD, Khiabanian H, Pasqualucci L, Dalla-Favera R

Nature. 2022.

PMID: 35794478
2
Tracking Immunoglobulin Repertoire and Transcriptomic Changes in Germinal Center B Cells by Single-Cell Analysis

Corinaldesi C, Holmes AB, Shen Q, Grunstein E, Pasqualucci L, Dalla-Favera R, Basso K

Frontiers in immunology. 2022.

PMID: 35095922
3
Mutations in the transcription factor FOXO1 mimic positive selection signals to promote germinal center B cell expansion and lymphomagenesis

Roberto MP, Varano G, Vinas-Castells R, Holmes AB, Kumar R, Pasqualucci L, Farinha P, Scott DW, Dominguez-Sola D

Immunity. 2021.

PMID: 34380064
4
miR-939 acts as tumor suppressor by modulating JUNB transcriptional activity in pediatric anaplastic large cell lymphoma

Garbin A, Lovisa F, Holmes AB, Damanti CC, Gallingani I, Carraro E, Accordi B, Veltri G, Pizzi M, d'Amore ESG, Pillon M, Biffi A, Basso K, Mussolin L

Haematologica. 2021.

PMID: 32299901
5
Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome

Holmes AB, Corinaldesi C, Shen Q, Kumar R, Compagno N, Wang Z, Nitzan M, Grunstein E, Pasqualucci L, Dalla-Favera R, Basso K

The Journal of experimental medicine. 2020.

PMID: 32603407
6
Unique and Shared Epigenetic Programs of the CREBBP and EP300 Acetyltransferases in Germinal Center B Cells Reveal Targetable Dependencies in Lymphoma

Meyer SN, Scuoppo C, Vlasevska S, Bal E, Holmes AB, Holloman M, Garcia-Ibanez L, Nataraj S, Duval R, Vantrimpont T, Basso K, Brooks N, Dalla-Favera R, Pasqualucci L

Immunity. 2019.

PMID: 31519498
7
MEF2B Instructs Germinal Center Development and Acts as an Oncogene in B Cell Lymphomagenesis

Brescia P, Schneider C, Holmes AB, Shen Q, Hussein S, Pasqualucci L, Basso K, Dalla-Favera R

Cancer cell. 2018.

PMID: 30205047
8
Common nonmutational NOTCH1 activation in chronic lymphocytic leukemia

Fabbri G, Holmes AB, Viganotti M, Scuoppo C, Belver L, Herranz D, Yan XJ, Kieso Y, Rossi D, Gaidano G, Chiorazzi N, Ferrando AA, Dalla-Favera R

Proceedings of the National Academy of Sciences. 2017.

PMID: 28314854
9
The CREBBP Acetyltransferase Is a Haploinsufficient Tumor Suppressor in B-cell Lymphoma

Zhang J, Vlasevska S, Wells VA, Nataraj S, Holmes AB, Duval R, Meyer SN, Mo T, Basso K, Brindle PK, Hussein S, Dalla-Favera R, Pasqualucci L

Cancer discovery. 2017.

PMID: 28069569
10
The genetics of nodal marginal zone lymphoma

Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbo F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foa R, Rabadan R, Gaidano G, Rossi D

Blood. 2016.

PMID: 27335277
11
Prognostic and therapeutic role of targetable lesions in B-lineage acute lymphoblastic leukemia without recurrent fusion genes

Messina M, Chiaretti S, Wang J, Fedullo AL, Peragine N, Gianfelici V, Piciocchi A, Brugnoletti F, Di Giacomo F, Pauselli S, Holmes AB, Puzzolo MC, Ceglie G, Apicella V, Mancini M, Te Kronnie G, Testi AM, Vitale A, Vignetti M, Guarini A, Rabadan R, Foa R

Oncotarget. 2016.

PMID: 26883104
12
The FOXO1 Transcription Factor Instructs the Germinal Center Dark Zone Program

Dominguez-Sola D, Kung J, Holmes AB, Wells VA, Mo T, Basso K, Dalla-Favera R

Immunity. 2015.

PMID: 26620759
13
Disruption of KMT2D perturbs germinal center B cell development and promotes lymphomagenesis

Zhang J, Dominguez-Sola D, Hussein S, Lee JE, Holmes AB, Bansal M, Vlasevska S, Mo T, Tang H, Basso K, Ge K, Dalla-Favera R, Pasqualucci L

Nature medicine. 2015.

PMID: 26366712
14
An aberrant microRNA signature in childhood T-cell lymphoblastic lymphoma affecting CDKN1B expression, NOTCH1 and growth factor signaling pathways

Mussolin L, Holmes AB, Romualdi C, Sales G, D'Amore ES, Ghisi M, Pillon M, Rosolen A, Basso K

Leukemia. 2014.

PMID: 24727675
15
MicroRNA 28 controls cell proliferation and is down-regulated in B-cell lymphomas

Schneider C, Setty M, Holmes AB, Maute RL, Leslie CS, Mussolin L, Rosolen A, Dalla-Favera R, Basso K

Proceedings of the National Academy of Sciences. 2014.

PMID: 24843176

See more on